1887

Abstract

Three strains (YZ01, YZ02 and YZ03) of Gram-stain-positive, facultatively anaerobic rods were isolated from the forestomach contents collected from a captive male proboscis monkey () at Yokohama Zoo in Japan. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belonged to the genus . Based on the sequence similarity of the 16S rRNA gene, subsp. JCM 15610 was the closest phylogenetic neighbour to YZ01. Sequence analyses of two partial concatenated housekeeping genes, the RNA polymerase alpha subunit () and phenylalanyl-tRNA synthase alpha subunit () also indicated that the novel strains belonged to the genus . The average nucleotide identity and digital DNA–DNA hybridization (dDDH) between subsp. and YZ01 were 85.9 and 31.4 %, respectively. The phylogenetic tree based on the whole genomic data of strains YZ01, YZ02 and YZ03 suggested that these three strains formed a single monophyletic cluster in the genus , indicating that it belonged to a new species. The DNA G+C content of strain YZ01 was 51.6 mol%. The major fatty acids were C and C ω9. Therefore, based on phylogenetic, phenotypic and physiological evidence, strains YZ01, YZ02 and YZ03 represent a novel species of the genus , for which the name sp. nov. is proposed with the type strain YZ01 (=JCM 33769=DSM 110539).

Funding
This study was supported by the:
  • Core Research for Evolutional Science and Technology (Award JPMJCR17A4)
    • Principle Award Recipient: IkkiMatsuda
  • Japan Society for the Promotion of Science (Award 19KK0186)
    • Principle Award Recipient: KazunariUshida
  • Japan Society for the Promotion of Science (Award 19H03308)
    • Principle Award Recipient: IkkiMatsuda
  • Japan Society for the Promotion of Science (Award 19K16241)
    • Principle Award Recipient: TakashiHayakawa
  • Japan Society for the Promotion of Science (Award 18K14590)
    • Principle Award Recipient: SayakaTsuchida
  • Japan Society for the Promotion of Science (Award 18J40006)
    • Principle Award Recipient: NamiSuzuki-Hashido
  • Japan Society for the Promotion of Science (Award 17K15203)
    • Principle Award Recipient: NamiSuzuki-Hashido
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004787
2021-04-27
2022-01-21
Loading full text...

Full text loading...

References

  1. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
    [Google Scholar]
  2. Duar RM, Lin XB, Zheng J, Martino ME, Grenier T et al. Lifestyles in transition: evolution and natural history of the genus Lactobacillus . FEMS Microbiol Rev 2017; 41:S27–S48 [View Article][PubMed]
    [Google Scholar]
  3. Zheng J, Wittouck S, Salvetti E, Franz CM, Harris HM et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae . Int J Syst Evol Microbiol 2020; 70:2782–2858 [View Article][PubMed]
    [Google Scholar]
  4. Endo A, Futagawa-Endo Y, Dicks LMT. Diversity of Lactobacillus and Bifidobacterium in feces of herbivores, omnivores and carnivores. Anaerobe 2010; 16:590–596 [View Article][PubMed]
    [Google Scholar]
  5. Tsuchida S, Kitahara M, Nguema PPM, Norimitsu S, Fujita S et al. Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild western lowland gorillas (Gorilla gorilla gorilla). Int J Syst Evol Microbiol 2014; 64:4001–4006 [View Article][PubMed]
    [Google Scholar]
  6. Tsuchida S, Murata K, Ohkuma M, Ushida K. Isolation of Streptococcus gallolyticus with very high degradability of condensed tannins from feces of the wild Japanese rock ptarmigans on Mt. Tateyama. J Gen Appl Microbiol 2017; 63:195–198 [View Article][PubMed]
    [Google Scholar]
  7. Matsuda I, Murai T, Clauss M, Yamada T, Tuuga A et al. Regurgitation and remastication in the foregut-fermenting proboscis monkey (Nasalis larvatus). Biol Lett 2011; 7:786–789 [View Article][PubMed]
    [Google Scholar]
  8. Hayakawa T, Nathan S, Stark DJ, Saldivar DAR, Sipangkui R et al. First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes?. Environ Microbiol Rep 2018; 10:655–662 [View Article][PubMed]
    [Google Scholar]
  9. Tsukahara T, Ushida K. Succinate accumulation in pig large intestine during antibiotic-associated diarrhea and the constitution of succinate-producing flora. J Gen Appl Microbiol 2002; 48:143–154 [View Article][PubMed]
    [Google Scholar]
  10. Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P et al. Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 2005; 151:2141–2150 [View Article][PubMed]
    [Google Scholar]
  11. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  12. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism 1969; 3:21–132
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  14. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  15. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  16. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
  17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  18. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  19. Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T et al. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2020; 27:dsaa014 [View Article][PubMed]
    [Google Scholar]
  20. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article]
    [Google Scholar]
  21. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  22. Katayama-Fujimura Y, Komatsu Y, Kuraishi H, Kaneko T. Estimation of DNA base composition by high performance liquid chromatography of its nuclease Pi hydrolysate. Agric Biol Chem 1984; 48:3169–3172 [View Article]
    [Google Scholar]
  23. Barrow GI, Feltham RKA. (editors) Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  24. Kawamoto I, Oka T, Nara T. Cell wall composition of Micromonospora olivoasterospora, Micromonospora sagamiensis, and related organisms. J Bacterol 1981; 146:527–534 [View Article][PubMed]
    [Google Scholar]
  25. Ahmed I, Kudo T, Abbas S, Ehsan M, Iino T, Fujiwara T et al. Cellulomonas pakistanensis sp. nov., a moderately halotolerant Actinobacteria. Int J Syst Evol Microbiol 2014; 64:2305–2311 [View Article][PubMed]
    [Google Scholar]
  26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  27. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics 2005; 21:2329–2335 [View Article][PubMed]
    [Google Scholar]
  28. Kudo Y, Oki K, Watanabe K. Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle. Int J Syst Evol Microbiol 2012; 62:2643–2649 [View Article][PubMed]
    [Google Scholar]
  29. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
    [Google Scholar]
  30. Unwin S, Ancrenaz M, Handling BW. Anaesthesia, health evaluation and biological sampling. In Setchell J, Curtis D. (editors) Field and Laboratory Methods in Primatology: A Practical Guide Cambridge: Cambridge University Press; 2011 pp 147–168
    [Google Scholar]
  31. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
    [Google Scholar]
  32. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article][PubMed]
    [Google Scholar]
  33. Kim JS, Choe H, Kim KM, Lee YR, Rhee MS et al. Lactobacillus porci sp. nov., isolated from small intestine of a swine. Int J Syst Evol Microbiol 2018; 68:3118–3124 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004787
Loading
/content/journal/ijsem/10.1099/ijsem.0.004787
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error